1 cmake_minimum_required(VERSION 2.8)
2 # Keep CMake suitably quiet on Cygwin
3 set(CMAKE_LEGACY_CYGWIN_WIN32 0) # Remove when CMake >= 2.8.4 is required
5 # CMake modules/macros are in a subdirectory to keep this file cleaner
6 # This needs to be set before project() in order to pick up toolchain files
7 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Platform)
11 mark_as_advanced(DART_ROOT)
13 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
14 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
15 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
17 # PROJECT_VERSION should have the following structure:
18 # VERSION-dev[-SUFFIX] where the VERSION should have the for: vMajor.vMinor.vPatch
20 # The "-dev" suffix is important to keep because it makes possible to distinguish
21 # between a build from official release and a build from git release branch on a
22 # machine with no git.
24 # NOTE: when releasing the "-dev" suffix needs to be stripped off!
25 set(PROJECT_VERSION "5.0-dev")
26 # The version number of the regressiontest tarball against which this
27 # git branch can be tested. Normally, this will be the version of the
28 # last patch release. Comment the next line out for branches leading
29 # to a major/minor release.
30 set(REGRESSIONTEST_VERSION "4.6.2")
31 set(CUSTOM_VERSION_STRING ""
32 CACHE STRING "Custom version string (if empty, use hard-coded default)")
33 mark_as_advanced(CUSTOM_VERSION_STRING)
34 if (CUSTOM_VERSION_STRING)
35 set(PROJECT_VERSION ${CUSTOM_VERSION_STRING})
36 endif (CUSTOM_VERSION_STRING)
38 # It is a bit irritating, but this has to be set separately for now!
39 SET(CPACK_PACKAGE_VERSION_MAJOR "5")
40 SET(CPACK_PACKAGE_VERSION_MINOR "0")
41 #SET(CPACK_PACKAGE_VERSION_PATCH "0")
43 # The numerical gromacs version. It is 40600 for 4.6.0.
44 # The #define GMX_VERSION in gmx_header_config_h is set to this value.
46 "${CPACK_PACKAGE_VERSION_MAJOR}*10000 + ${CPACK_PACKAGE_VERSION_MINOR}*100")
47 if(CPACK_PACKAGE_VERSION_PATCH)
49 "${NUM_VERSION} + ${CPACK_PACKAGE_VERSION_PATCH}")
52 # The API version tracks the numerical Gromacs version (for now).
53 # It is potentially different from the Gromacs version in the future, if
54 # the programs/libraries diverge from the presumably more stable API.
55 # The #define GMX_API_VERSION in version.h is set to this value to
56 # provide backward compatibility of software written against the Gromacs API.
57 set(API_VERSION ${NUM_VERSION})
59 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
60 set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
63 set(GMX_INSTALL_PREFIX "" CACHE STRING "Prefix gets appended to CMAKE_INSTALL_PREFIX. For cpack it sets the root folder of the archive.")
64 mark_as_advanced(GMX_INSTALL_PREFIX)
66 include(gmxBuildTypeReference)
68 if(NOT CMAKE_BUILD_TYPE)
69 set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference." FORCE)
70 endif(NOT CMAKE_BUILD_TYPE)
75 set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
76 set(CPACK_PACKAGE_VENDOR "gromacs.org")
77 set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
78 set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
79 # Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
80 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
81 set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
82 set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$")
83 set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
84 SET(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/man;man")
85 set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
87 #must come after all cpack settings!
90 set(SOURCE_IS_GIT_REPOSITORY OFF)
91 if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
92 set(SOURCE_IS_GIT_REPOSITORY ON)
95 ########################################################################
96 # Check and warn if cache generated on a different host is being reused
97 ########################################################################
99 execute_process(COMMAND hostname
100 OUTPUT_VARIABLE TMP_HOSTNAME
101 OUTPUT_STRIP_TRAILING_WHITESPACE)
102 if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
104 The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
105 is being reused! This could lead to inconsitencies; therefore, it is
106 recommended to regenerate the cache!")
108 set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
109 "Hostname of the machine where the cache was generated.")
112 ########################################################################
113 # User input options #
114 ########################################################################
115 include(gmxOptionUtilities)
117 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
119 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
120 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
121 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
122 gmx_dependent_option(
124 "Enable MPI_IN_PLACE for MPIs that have it defined"
127 mark_as_advanced(GMX_MPI_IN_PLACE)
128 option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
129 mark_as_advanced(GMX_SOFTWARE_INVSQRT)
130 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
131 mark_as_advanced(GMX_FAHCORE)
133 option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
134 mark_as_advanced(GMX_COOL_QUOTES)
135 gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
137 # decide on GPU settings based on user-settings and GPU/CUDA detection
138 include(gmxManageGPU)
140 include(gmxDetectAcceleration)
141 set(GMX_SUGGESTED_CPU_ACCELERATION "None")
142 if(NOT DEFINED GMX_CPU_ACCELERATION)
143 if(CMAKE_CROSSCOMPILING)
144 if("${CMAKE_SYSTEM_NAME}" MATCHES "BlueGeneQ")
145 set(GMX_SUGGESTED_CPU_ACCELERATION "IBM_QPX")
147 set(GMX_SUGGESTED_CPU_ACCELERATION "None")
149 else(CMAKE_CROSSCOMPILING)
150 gmx_detect_acceleration(GMX_SUGGESTED_CPU_ACCELERATION)
151 endif(CMAKE_CROSSCOMPILING)
152 endif(NOT DEFINED GMX_CPU_ACCELERATION)
154 gmx_option_multichoice(
156 "Acceleration for CPU kernels and compiler optimization"
157 "${GMX_SUGGESTED_CPU_ACCELERATION}"
158 None SSE2 SSE4.1 AVX_128_FMA AVX_256 IBM_QPX Sparc64_HPC_ACE)
160 gmx_option_multichoice(
164 fftw3 mkl "fftpack[built-in]")
165 gmx_dependent_option(
167 "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
169 "GMX_FFT_LIBRARY STREQUAL FFTW3")
170 gmx_dependent_option(
171 GMX_DISABLE_FFTW_MEASURE
172 "Do not optimize FFTW setups (not needed with SSE)"
174 "GMX_FFT_LIBRARY STREQUAL FFTW3")
175 mark_as_advanced(GMX_BUILD_OWN_FFTW)
176 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
178 gmx_option_multichoice(
180 "QM package for QM/MM"
182 none gaussian mopac gamess orca)
184 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
185 mark_as_advanced(GMX_BROKEN_CALLOC)
186 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
187 mark_as_advanced(GMX_LOAD_PLUGINS)
189 option(GMX_GPU "Enable GPU acceleration" ON)
190 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
192 option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
193 mark_as_advanced(GMX_GIT_VERSION_INFO)
196 option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
198 option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
201 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static archives (not available on non-*nix platforms and it will only work if static versions of external dependencies are available and found)!" OFF)
202 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
205 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
206 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
208 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
209 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
211 option(GMX_BUILD_FOR_COVERAGE
212 "Tune build for better code coverage metrics (e.g., disable asserts)"
214 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
216 ######################################################################
218 # These need to be done early (before further tests).
219 #####################################################################
221 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
222 # are used with permission from CMake v2.8.9 so that GROMACS can detect
223 # invalid options with the Intel Compilers.
224 # These files should be removed from the source tree when a CMake version that
225 # includes the features in question becomes required for building GROMACS.
226 include(CheckCCompilerFlag)
227 include(CheckCXXCompilerFlag)
229 # Get compiler version information, needs to be done early as check that depend
230 # on compiler verison follow below.
231 include(gmxGetCompilerInfo)
232 get_compiler_version()
234 # First exclude compilers known to not work with OpenMP although claim to support it:
235 # gcc 4.2.1 and gcc-llvm 4.2.1 (also claims to be 4.2.1) on Mac OS X
236 # This fixes redmine 900 and needs to run before OpenMP flags are set below.
237 if (CMAKE_SYSTEM_NAME STREQUAL "Darwin" AND
238 (CMAKE_COMPILER_IS_GNUCC AND C_COMPILER_VERSION AND C_COMPILER_VERSION VERSION_LESS 4.3))
239 message(STATUS "OpenMP multithreading not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled")
240 set(GMX_OPENMP OFF CACHE BOOL
241 "OpenMP multithreading not not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled!" FORCE)
244 # OpenMP check must come before other CFLAGS!
248 # CMake on Windows doesn't support linker flags passed to target_link_libraries
249 # (i.e. it treats /openmp as \openmp library file). Also, no OpenMP linker flags are needed.
250 if(NOT (WIN32 AND NOT CYGWIN))
251 if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP AND NOT APPLE)
252 set(OpenMP_LINKER_FLAGS "-Wl,-static -lgomp -lrt -Wl,-Bdynamic -lpthread")
253 set(OpenMP_SHARED_LINKER_FLAGS "")
255 # Only set a linker flag if the user didn't set them manually
256 if(NOT DEFINED OpenMP_LINKER_FLAGS)
257 set(OpenMP_LINKER_FLAGS "${OpenMP_C_FLAGS}")
259 if(NOT DEFINED OpenMP_SHARED_LINKER_FLAGS)
260 set(OpenMP_SHARED_LINKER_FLAGS "${OpenMP_C_FLAGS}")
266 "The compiler you are using does not support OpenMP parallelism. This might hurt your performance a lot, in particular with GPUs. Try using a more recent version, or a different compiler. For now, we are proceeding by turning off OpenMP.")
267 set(GMX_OPENMP OFF CACHE STRING "Whether GROMACS will use OpenMP parallelism." FORCE)
275 # This variable should be used for additional compiler flags which are not
276 # generated in gmxCFlags nor are acceleration or MPI related.
277 set(EXTRA_C_FLAGS "")
278 set(EXTRA_CXX_FLAGS "")
280 # gcc 4.4.x is buggy and crashes when compiling some files with O3 and OpenMP on.
281 # Detect here whether applying a workaround is needed and will apply it later
282 # on the affected files.
283 include(gmxGCC44O3BugWorkaround)
284 gmx_check_gcc44_bug_workaround_needed(GMX_USE_GCC44_BUG_WORKAROUND)
286 # clang 3.0 is buggy for some unknown reason detected during adding
287 # the SSE2 group kernels for GROMACS 4.6. If we ever work out what
288 # that is, we should replace these tests with a compiler feature test,
289 # update GROMACS Redmine task #1039 and perhaps report a clang bug.
291 # In the meantime, until we require CMake 2.8.10 we cannot rely on it to detect
292 # the compiler version for us. So we need a manual check for clang 3.0.
293 include(gmxDetectClang30)
294 gmx_detect_clang_3_0(COMPILER_IS_CLANG_3_0)
295 if(COMPILER_IS_CLANG_3_0)
296 message(FATAL_ERROR "Your compiler is clang version 3.0, which is known to be buggy for GROMACS. Use a different compiler.")
299 # clang <=3.2 contains a bug that causes incorrect code to be generated for the
300 # vfmaddps instruction and therefore the bug is triggered with AVX_128_FMA.
301 # (see: http://llvm.org/bugs/show_bug.cgi?id=15040).
302 # We can work around this by not using the integrated assembler (except on OS X
303 # which has an outdated assembler that does not support AVX instructions).
304 if (${CMAKE_C_COMPILER_ID} MATCHES "Clang" AND C_COMPILER_VERSION VERSION_LESS "3.3")
305 set(GMX_USE_CLANG_C_FMA_BUG_WORKAROUND TRUE)
307 if (${CMAKE_CXX_COMPILER_ID} MATCHES "Clang" AND CXX_COMPILER_VERSION VERSION_LESS "3.3")
308 set(GMX_USE_CLANG_CXX_FMA_BUG_WORKAROUND TRUE)
311 if (CMAKE_C_COMPILER_ID STREQUAL "PGI")
312 message(WARNING "All tested PGI compiler versions (up to 12.9.0) generate binaries which produce incorrect results, or even fail to compile Gromacs. Highly recommended to use a different compiler. If you choose to use PGI, make sure to run the regressiontests.")
315 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_LESS "12.0.0")
316 message(WARNING "Intel compilers before 12.0.0 are not routinely tested, so there may be problems. Version 11.1 with SSE4.1 is known to produce incorrect results. It is highly recommended to use a more up-to-date compiler. If you choose to use this version, make sure you run the regressiontests.")
321 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
323 if(GMX_SOFTWARE_INVSQRT)
324 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
325 endif(GMX_SOFTWARE_INVSQRT)
329 ########################################################################
330 # Basic system tests (standard libraries, headers, functions, types) #
331 ########################################################################
332 include(CheckIncludeFiles)
333 include(CheckIncludeFileCXX)
334 check_include_files(unistd.h HAVE_UNISTD_H)
335 check_include_files(pwd.h HAVE_PWD_H)
336 check_include_files(dirent.h HAVE_DIRENT_H)
337 check_include_files(sys/time.h HAVE_SYS_TIME_H)
338 check_include_files(io.h HAVE_IO_H)
339 check_include_files(sched.h HAVE_SCHED_H)
341 check_include_files(regex.h HAVE_POSIX_REGEX)
342 check_include_file_cxx(regex HAVE_CXX11_REGEX)
343 # TODO: It could be nice to inform the user if no regex support is found,
344 # as selections won't be fully functional.
346 include(CheckFunctionExists)
347 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
348 check_function_exists(memalign HAVE_MEMALIGN)
349 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
350 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
351 check_function_exists(fsync HAVE_FSYNC)
352 check_function_exists(_fileno HAVE__FILENO)
353 check_function_exists(fileno HAVE_FILENO)
354 check_function_exists(_commit HAVE__COMMIT)
355 check_function_exists(sigaction HAVE_SIGACTION)
356 check_function_exists(sysconf HAVE_SYSCONF)
357 check_function_exists(sched_setaffinity HAVE_SCHED_SETAFFINITY)
358 check_function_exists(sched_getaffinity HAVE_SCHED_GETAFFINITY)
359 check_function_exists(rsqrt HAVE_RSQRT)
360 check_function_exists(rsqrtf HAVE_RSQRTF)
361 check_function_exists(sqrtf HAVE_SQRTF)
363 include(CheckLibraryExists)
364 check_library_exists(m sqrt "" HAVE_LIBM)
367 include(CheckTypeSize)
369 check_type_size("int" SIZEOF_INT)
370 check_type_size("long int" SIZEOF_LONG_INT)
371 check_type_size("long long int" SIZEOF_LONG_LONG_INT)
372 check_type_size("off_t" SIZEOF_OFF_T)
373 check_type_size("void *" SIZEOF_VOIDP)
375 include(TestBigEndian)
376 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
379 if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD")
380 # Maybe Solaris should be here? Patch this if you know!
381 SET(SHARED_LIBS_DEFAULT ON)
382 elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
383 # Support for shared libs on native Windows is a bit new. Its
384 # default might change later if/when we sort things out. Also,
385 # Cray should go here. What variable value can detect it?
386 SET(SHARED_LIBS_DEFAULT OFF)
388 message(STATUS "Defaulting to building static libraries")
389 SET(SHARED_LIBS_DEFAULT OFF)
392 # Management of GROMACS options for specific toolchains should go
393 # here. Because the initial settings for some of the main options have
394 # already happened, but things like library detection and MPI compiler
395 # feature detection have not, the docstrings for any over-rides of
396 # GROMACS defaults or user settings will make sense. Also, any
397 # toolchain-related reasons for choosing whether to detect various
398 # things can be sorted out now, before the detection takes place.
399 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
400 include(gmxManageBlueGene)
403 if(UNIX AND GMX_PREFER_STATIC_LIBS AND SHARED_LIBS_DEFAULT)
404 if(BUILD_SHARED_LIBS)
405 # Warn the user about the combination. But don't overwrite the request.
406 message(WARNING "Searching for static libraries requested, and building shared Gromacs libraries requested. This might cause problems linking later.")
407 elseif(NOT DEFINED BUILD_SHARED_LIBS)
408 # Change default to OFF. Don't warn if it's already off.
409 message(WARNING "Searching for static libraries requested, so the GROMACS libraries will also be built statically (BUILD_SHARED_LIBS=OFF)")
410 set(SHARED_LIBS_DEFAULT OFF)
414 # By now, all tool chains should have spoken up if they care about
415 # the setting of SHARED_LIBS_DEFAULT.
416 option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic e.g. with MPI, or on some HPC systems)" ${SHARED_LIBS_DEFAULT})
418 ########################################################################
419 #Process MPI settings
420 ########################################################################
421 include(gmxManageMPI)
423 ########################################################################
424 # Find external packages #
425 ########################################################################
426 if(UNIX AND GMX_PREFER_STATIC_LIBS)
427 # On Linux .a is the static library suffix, on Mac OS X .lib can also
428 # be used, so we'll add both to the preference list.
429 SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib;.a" ${CMAKE_FIND_LIBRARY_SUFFIXES})
432 IF( WIN32 AND NOT CYGWIN)
433 # This makes windows.h not declare min/max as macros that would break
434 # C++ code using std::min/std::max.
435 add_definitions(-DNOMINMAX)
437 if (NOT BUILD_SHARED_LIBS)
438 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" ON)
439 if(NOT GMX_PREFER_STATIC_LIBS)
440 message(WARNING "Shared system libraries requested, and static Gromacs libraries requested.")
443 message(FATAL_ERROR "BUILD_SHARED_LIBS not yet working for Windows in the master branch")
444 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" OFF)
445 if(GMX_PREFER_STATIC_LIBS)
446 #this combination segfaults (illigal passing of file handles)
447 message(FATAL_ERROR "Static system libraries requested, and shared Gromacs libraries requested.")
449 add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
450 set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
452 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
454 IF (GMX_PREFER_STATIC_LIBS)
455 #Only setting Debug and Release flags. Others configurations are current not used.
456 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
457 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
458 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
459 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
461 IF( CMAKE_C_COMPILER_ID MATCHES "Intel" )
462 if(BUILD_SHARED_LIBS) #not sure why incremental building with shared libs doesn't work
463 STRING(REPLACE "/INCREMENTAL:YES" "" CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS})
468 # Unconditionally find the package, as it is also required for unit tests
469 find_package(LibXml2)
470 option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${LIBXML2_FOUND})
472 mark_as_advanced(GMX_XML)
473 # Don't actually do anything, since libxml2 is currently not used by libgromacs
474 #if(GMX_XML AND NOT LIBXML2_FOUND)
475 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
478 # include_directories(${LIBXML2_INCLUDE_DIR})
479 # set(PKG_XML libxml-2.0)
480 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
483 option(GMX_GSL "Add support for gsl" OFF)
488 include_directories(${GSL_INCLUDE_DIR})
494 option(GMX_X11 "Use X window system" OFF)
497 # X11 includes/libraries are only set in the ngmx subdirectory!
499 message(WARNING "X11 include files and/or libraries were not found. Will not build the GROMACS X11-binaries, such as ngmx")
502 include_directories(${X11_INCLUDE_DIR})
507 set(THREAD_MPI_LIB thread_mpi)
508 # Enable core threading facilities
509 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders")
510 # Enable tMPI C++ support
513 # enable MPI functions
515 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
517 endif(GMX_THREAD_MPI)
518 tmpi_get_source_list(THREAD_MPI_SRC)
521 # now that we have detected the dependencies, do the second configure pass
529 if(WIN32 AND NOT CYGWIN)
530 set(GMX_NATIVE_WINDOWS 1)
533 # only bother with finding git and using version.h if the source is a git repo
534 if(GMX_GIT_VERSION_INFO)
535 if (NOT SOURCE_IS_GIT_REPOSITORY)
537 "Cannot generate git version information from source tree not under git. "
538 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
540 # We need at least git v1.5.3 be able to parse git's date output. If not
541 # found or the version is too small, we can't generate version information.
544 # Find out the git version
545 if(GIT_FOUND AND NOT GIT_VERSION)
546 execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
547 OUTPUT_VARIABLE _exec_out
548 OUTPUT_STRIP_TRAILING_WHITESPACE)
549 string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
550 set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
551 mark_as_advanced(GIT_VERSION)
554 if(NOT GIT_FOUND OR GIT_VERSION VERSION_LESS "1.5.3")
556 "No compatible git version found (>= 1.5.3 required). "
557 "Won't be able to generate development version information. "
558 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
562 # Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
563 # Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
564 if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
565 find_package(Boost 1.44.0)
566 if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
567 set(Boost_FOUND FALSE)
569 # Print the notification only on first run, when determining the default
570 if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
571 message("Boost >= 1.44 not found. Using minimal internal version. "
572 "This may cause trouble if you plan on compiling/linking other "
573 "software that uses Boost against Gromacs.")
576 option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
578 if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
580 "Boost >= 1.44 not found. "
581 "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
582 "version of Boost included with Gromacs.")
585 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${LIBXML2_FOUND})
586 mark_as_advanced(GMX_BUILD_UNITTESTS)
587 gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
588 if (GMX_BUILD_UNITTESTS AND NOT LIBXML2_FOUND)
590 "Cannot build unit tests without libxml2. "
591 "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find libxml2.")
593 set(MEMORYCHECK_SUPPRESSIONS_FILE ${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp)
595 ########################################################################
596 # Generate development version info for cache
597 ########################################################################
598 # set(GEN_VERSION_INFO_INTERNAL "ON")
599 # include(gmxGenerateVersionString)
601 ########################################################################
602 # Our own GROMACS tests
603 ########################################################################
605 add_definitions( -DHAVE_CONFIG_H )
606 include_directories(${CMAKE_SOURCE_DIR}/src)
607 # Required for config.h, maybe should only be set in src/CMakeLists.txt
608 include_directories(${CMAKE_BINARY_DIR}/src)
609 # Required for gmx_header_config_gen.h to be found before installation
610 include_directories(${CMAKE_BINARY_DIR}/src/gromacs/utility)
611 # Required for now to make old code compile
612 include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
614 include(gmxTestInlineASM)
615 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
617 include(gmxSetBuildInformation)
618 gmx_set_build_information()
619 if(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
620 # The timestep counter headers do not include config.h
621 add_definitions(-DHAVE_RDTSCP)
622 endif(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
624 include(gmxTestFloatFormat)
625 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
626 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
627 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
629 include(gmxTestLargeFiles)
630 gmx_test_large_files(GMX_LARGEFILES)
632 include(gmxTestSignal)
633 gmx_test_sigusr1(HAVE_SIGUSR1)
635 include(gmxTestInline)
636 gmx_test_inline(INLINE_KEYWORD)
638 include(gmxTestRestrict)
639 gmx_test_restrict(RESTRICT_KEYWORD)
641 include(gmxTestPipes)
642 gmx_test_pipes(HAVE_PIPES)
644 include(gmxTestIsfinite)
645 gmx_test_isfinite(HAVE_ISFINITE)
646 gmx_test__isfinite(HAVE__ISFINITE)
647 gmx_test__finite(HAVE__FINITE)
649 include(gmxTestCXX11)
650 gmx_test_cxx11(GMX_CXX11 GMX_CXX11_FLAGS)
651 if(CXX11_FLAG AND GMX_GPU)
652 #FIXME: add proper solution for progate all but cxx11 flag
653 set(CUDA_PROPAGATE_HOST_FLAGS no)
654 message(WARNING "Please manually add compiler flags to CUDA_NVCC_FLAGS. Automatic propogation temporary not working.")
658 gmx_test_xdr(GMX_SYSTEM_XDR)
659 if(NOT GMX_SYSTEM_XDR)
660 set(GMX_INTERNAL_XDR 1)
661 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_INTERNAL_XDR")
662 endif(NOT GMX_SYSTEM_XDR)
664 # include avx test source, used if the AVX flags are set below
665 include(gmxTestAVXMaskload)
667 # Process nonbonded accelerated kernels settings
669 # Note that for the backward-compatible x86 SIMD architectures, the
670 # GMX_CPU_ACCELERATION determines the maximum level of the instruction
671 # set used (e.g. GMX_CPU_ACCLERATION=SSE4.1 implies
672 # SSE2). Accordingly, there are a set of CMake variables
673 # GMX_<arch>_<feature-set> that are exported to the C code to specify
674 # CPU features that should be used. This means that the logic for
675 # requiring such backward compatibility is all located here.
676 if(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
678 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE2")
680 GMX_TEST_CFLAG(GNU_SSE2_CFLAG "-msse2" ACCELERATION_C_FLAGS)
681 if(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
682 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
683 endif(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
685 GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" ACCELERATION_CXX_FLAGS)
686 if(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
687 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
688 endif(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
690 # We dont warn for lacking SSE2 flag support, since that is probably standard today.
692 # Only test the include after we have tried to add the correct flag for SSE2 support
693 check_include_file(emmintrin.h HAVE_EMMINTRIN_H ${ACCELERATION_C_FLAGS})
695 if(NOT HAVE_EMMINTRIN_H)
696 message(FATAL_ERROR "Cannot find emmintrin.h, which is required for SSE2 intrinsics support.")
697 endif(NOT HAVE_EMMINTRIN_H)
699 set(GMX_CPU_ACCELERATION_X86_SSE2 1)
700 # The user should not be able to set this orthogonally to the acceleration
702 if (NOT ACCELERATION_QUIETLY)
703 message(STATUS "Enabling SSE2 Gromacs acceleration, and it will help compiler optimization.")
706 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE4.1")
708 GMX_TEST_CFLAG(GNU_SSE4_CFLAG "-msse4.1" ACCELERATION_C_FLAGS)
709 if (NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
710 GMX_TEST_CFLAG(MSVC_SSE4_CFLAG "/arch:SSE4.1" ACCELERATION_C_FLAGS)
711 endif(NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
712 if (NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
713 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
714 # intrinsics when SSE2 support is enabled, so we try that instead first.
715 if (GMX_NATIVE_WINDOWS)
716 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
717 message(WARNING "Neither SSE4.1 or SSE2 seems to be supported by your Windows compiler. Something is likely broken.")
719 message(WARNING "No C SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance")
721 endif(NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
723 GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" ACCELERATION_CXX_FLAGS)
724 if (NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
725 GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" ACCELERATION_CXX_FLAGS)
726 endif(NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
727 if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
728 message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance.")
729 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
730 # intrinsics when SSE2 support is enabled, so we try that instead.
731 if (GMX_NATIVE_WINDOWS)
732 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
734 endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
736 # This must come after we have added the -msse4.1 flag on some platforms.
737 check_include_file(smmintrin.h HAVE_SMMINTRIN_H ${ACCELERATION_C_FLAGS})
739 if(NOT HAVE_SMMINTRIN_H)
740 message(FATAL_ERROR "Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support.")
741 endif(NOT HAVE_SMMINTRIN_H)
743 set(GMX_CPU_ACCELERATION_X86_SSE4_1 1)
744 # The user should not be able to set this orthogonally to the acceleration
745 set(GMX_X86_SSE4_1 1)
747 if (NOT ACCELERATION_QUIETLY)
748 message(STATUS "Enabling SSE4.1 Gromacs acceleration, and it will help compiler optimization.")
751 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_EQUAL "11.1")
752 message(FATAL_ERROR "You are using Intel compiler version 11.1, and that compiler is known to produce incorrect results with SSE4.1 acceleration. You need to use another compiler (e.g. icc 12 or newer) or different acceleration (probably slower simulations).")
754 elseif(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" OR ${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
756 # Set the AVX compiler flag for both these choices!
758 GMX_TEST_CFLAG(GNU_AVX_CFLAG "-mavx" ACCELERATION_C_FLAGS)
759 if (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
760 GMX_TEST_CFLAG(MSVC_AVX_CFLAG "/arch:AVX" ACCELERATION_C_FLAGS)
761 endif (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
762 if (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
763 message(WARNING "No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance) giving the -DGMX_CPU_ACCELERATION=SSE4.1 to cmake.")
764 endif (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
766 GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" ACCELERATION_CXX_FLAGS)
767 if (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
768 GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" ACCELERATION_CXX_FLAGS)
769 endif (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
770 if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
771 message(WARNING "No C++ AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance) giving the -DGMX_CPU_ACCELERATION=SSE4.1 to cmake.")
772 endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
774 # Set the FMA4 flags (MSVC doesn't require any)
775 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" AND NOT MSVC)
776 GMX_TEST_CFLAG(GNU_FMA_CFLAG "-mfma4" ACCELERATION_C_FLAGS)
777 if (NOT GNU_FMA_CFLAG)
778 message(WARNING "No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
779 endif(NOT GNU_FMA_CFLAG)
780 GMX_TEST_CFLAG(GNU_XOP_CFLAG "-mxop" ACCELERATION_C_FLAGS)
781 # No big deal if we do not have xop, so no point yelling warnings about it.
782 GMX_TEST_CXXFLAG(GNU_FMA_CXXFLAG "-mfma4" ACCELERATION_CXX_FLAGS)
783 if (NOT GNU_FMA_CXXFLAG)
784 message(WARNING "No C++ FMA flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
785 endif (NOT GNU_FMA_CXXFLAG)
786 GMX_TEST_CXXFLAG(GNU_XOP_CXXFLAG "-mxop" ACCELERATION_CXX_FLAGS)
787 # No big deal if we do not have xop, so no point yelling warnings about it.
790 # Only test the header after we have tried to add the flag for AVX support
791 check_include_file(immintrin.h HAVE_IMMINTRIN_H ${ACCELERATION_C_FLAGS})
793 if(NOT HAVE_IMMINTRIN_H)
794 message(FATAL_ERROR "Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler.")
795 endif(NOT HAVE_IMMINTRIN_H)
797 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
798 try_compile(TEST_AVX ${CMAKE_BINARY_DIR}
799 "${CMAKE_SOURCE_DIR}/cmake/TestAVX.c"
800 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
802 message(FATAL_ERROR "Cannot compile AVX intrinsics. Consider switching compiler.")
806 # GCC requires x86intrin.h for FMA support. MSVC 2010 requires intrin.h for FMA support.
807 check_include_file(x86intrin.h HAVE_X86INTRIN_H ${ACCELERATION_C_FLAGS})
808 check_include_file(intrin.h HAVE_INTRIN_H ${ACCELERATION_C_FLAGS})
810 # The user should not be able to set this orthogonally to the acceleration
811 set(GMX_X86_SSE4_1 1)
814 # But just enable one of the choices internally...
815 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA")
816 set(GMX_CPU_ACCELERATION_X86_AVX_128_FMA 1)
817 set(GMX_X86_AVX_128_FMA 1)
818 if (NOT ACCELERATION_QUIETLY)
819 message(STATUS "Enabling 128-bit AVX Gromacs acceleration (with fused-multiply add), and it will help compiler optimization.")
822 # We don't have the full compiler version string yet (BUILD_C_COMPILER),
823 # so we can't distinguish vanilla and Apple clang, but catering for AMD
824 # hackintoshes is not worth the effort.
825 if (APPLE AND (${CMAKE_C_COMPILER_ID} STREQUAL "Clang" OR
826 ${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
827 message(WARNING "Due to a known compiler bug, Clang up to version 3.2 (and Apple Clang up to version 4.1) produces incorrect code with AVX_128_FMA acceleration. As we can not work around this bug on OS X, you will have to select a different compiler or CPU acceleration.")
830 if (GMX_USE_CLANG_C_FMA_BUG_WORKAROUND)
831 # we assume that we have an external assembler that supports AVX
832 message(STATUS "Clang ${C_COMPILER_VERSION} detected, enabling FMA bug workaround")
833 set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} -no-integrated-as")
835 if (GMX_USE_CLANG_CXX_FMA_BUG_WORKAROUND)
836 # we assume that we have an external assembler that supports AVX
837 message(STATUS "Clang ${CXX_COMPILER_VERSION} detected, enabling FMA bug workaround")
838 set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} -no-integrated-as")
842 # If we are not doing AVX_128, it must be AVX_256...
843 set(GMX_CPU_ACCELERATION_X86_AVX_256 1)
844 set(GMX_X86_AVX_256 1)
845 if (NOT ACCELERATION_QUIETLY)
846 message(STATUS "Enabling 256-bit AVX Gromacs acceleration, and it will help compiler optimization.")
850 # Unfortunately gcc-4.5.2 and gcc-4.6.0 has a bug where they use the wrong datatype for the formal
851 # parameter of the mask for maskload/maskstore arguments. Check if this is present, since we can work around it.
852 gmx_test_avx_gcc_maskload_bug(${ACCELERATION_C_FLAGS} GMX_X86_AVX_GCC_MASKLOAD_BUG)
854 elseif(${GMX_CPU_ACCELERATION} STREQUAL "IBM_QPX")
856 if (CMAKE_C_COMPILER_ID MATCHES "XL")
857 GMX_TEST_CFLAG(XLC_BLUEGENEQ_CFLAG "-qarch=qp -qtune=qp" ACCELERATION_C_FLAGS)
858 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
859 "${CMAKE_SOURCE_DIR}/cmake/TestQPX.c"
860 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
862 message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics.")
865 if (CMAKE_CXX_COMPILER_ID MATCHES "XL")
866 GMX_TEST_CXXFLAG(XLC_BLUEGENEQ_CXXFLAG "-qarch=qp -qtune=qp" ACCELERATION_CXX_FLAGS)
867 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
868 "${CMAKE_SOURCE_DIR}/cmake/TestQPX.c"
869 COMPILE_DEFINITIONS "${ACCELERATION_CXX_FLAGS}")
871 message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics.")
876 message(WARNING "IBM QPX acceleration was selected and could be compiled, but the accelerated kernels are not yet available.")
877 set(GMX_CPU_ACCELERATION_IBM_QPX 1)
879 message(FATAL_ERROR "Cannot compile IBM QPX intrinsics without the XL compiler. If you are compiling for BlueGene/Q, use 'cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C' to set up the tool chain.")
881 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SPARC64_HPC_ACE")
882 set(GMX_CPU_ACCELERATION_SPARC64_HPC_ACE 1)
884 gmx_invalid_option_value(GMX_CPU_ACCELERATION)
886 set(ACCELERATION_QUIETLY TRUE CACHE INTERNAL "")
888 # Process QM/MM Settings
889 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
890 set(GMX_QMMM_GAUSSIAN 1)
891 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
892 set(GMX_QMMM_MOPAC 1)
893 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
894 set(GMX_QMMM_GAMESS 1)
895 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
897 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
900 gmx_invalid_option_value(GMX_QMMM_PROGRAM)
903 # Process FFT library settings
906 # Intel 11 and up makes life somewhat easy if you just want to use
907 # all their stuff. It's not easy if you only want some of their
909 set(MKL_MANUALLY FALSE)
910 if (GMX_FFT_LIBRARY STREQUAL "MKL" AND
911 NOT (CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_GREATER "11"))
912 # The user will have to provide the set of magic libraries in
913 # MKL_LIBRARIES (see below), which we cache (non-advanced), so that they
914 # don't have to keep specifying it, and can easily see that
915 # CMake is still using that information.
916 set(MKL_MANUALLY TRUE)
918 set(MKL_LIBRARIES_FORMAT_DESCRIPTION "Use full paths to library files, in the right order, and separated by semicolons.")
919 gmx_dependent_cache_variable(
921 "List of libraries for linking to MKL. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}"
924 gmx_dependent_cache_variable(
926 "Path to mkl.h (non-inclusive)."
929 if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
936 if(GMX_BUILD_OWN_FFTW)
937 add_subdirectory(src/contrib/fftw)
939 find_package(FFTW COMPONENTS ${FFTW})
942 string(TOUPPER "${FFTW}" FFTW)
943 if(NOT ${FFTW}_FOUND)
944 MESSAGE(FATAL_ERROR "Cannot find FFTW 3 (with correct precision - libfftw3f for single-precision GROMACS or libfftw3 for double-precision GROMACS). Either choose the right precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the advanced option to let GROMACS build FFTW 3 for you (-DGMX_BUILD_OWN_FFTW=ON) , or use the really slow GROMACS built-in fftpack library (-DGMX_FFT_LIBRARY=fftpack).")
947 set(PKG_FFT "${${FFTW}_PKG}")
948 include_directories(${${FFTW}_INCLUDE_DIRS})
949 set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
952 if ((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND NOT ${FFTW}_HAVE_SIMD)
953 message(WARNING "The fftw library found is compiled without SIMD support, which makes it slow. Consider recompiling it or contact your admin")
956 if((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND ${FFTW}_HAVE_AVX)
957 # If we're not doing CPU acceleration, we don't care about FFTW performance on x86 either
958 message(WARNING "The FFTW library was compiled with --enable-avx to enable AVX SIMD instructions. That might sound like a good idea for your processor, but for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD instructions for the way GROMACS uses FFTs. Limitations in the way FFTW allows GROMACS to measure performance make it awkward for either GROMACS or FFTW to make the decision for you based on runtime performance. You should compile a different FFTW library with --enable-sse or --enable-sse2. If you have a more recent FFTW, you may like to compare the performance of GROMACS with FFTW libraries compiled with and without --enable-avx. However, the GROMACS developers do not really expect the FFTW AVX optimization to help, because the performance is limited by memory access, not computation.")
961 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
962 MESSAGE(STATUS "Using external FFT library - FFTW3")
964 elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
965 # Intel 11 and up makes life somewhat easy if you just want to use
966 # all their stuff. It's not easy if you only want some of their
968 if (NOT MKL_MANUALLY)
969 # The next line takes care of everything for MKL
971 set(FFT_LINKER_FLAGS "/Qmkl=sequential")
973 set(FFT_LINKER_FLAGS "-mkl=sequential")
975 # Some versions of icc require this in order that mkl.h can be
976 # found at compile time.
977 set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} ${FFT_LINKER_FLAGS}")
979 set(MKL_ERROR_MESSAGE "Make sure you have configured your compiler so that ${FFT_LINKER_FLAGS} will work.")
981 include_directories(${MKL_INCLUDE_DIR})
982 set(FFT_LIBRARIES "${MKL_LIBRARIES}")
983 set(MKL_ERROR_MESSAGE "The include path to mkl.h in MKL_INCLUDE_DIR, and the link libraries in MKL_LIBRARIES=${MKL_LIBRARIES} need to match what the MKL documentation says you need for your system. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
984 # Convert the semi-colon separated list to a list of
985 # command-line linker arguments so that code using our
986 # pkgconfig setup can use it.
987 string(REGEX REPLACE ";" " " PKG_FFT_LIBS "${MKL_LIBRARIES}")
990 # Check MKL works. If we were in a non-global scope, we wouldn't
991 # have to play nicely.
992 set(old_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
993 set(CMAKE_REQUIRED_FLAGS "${FFT_LINKER_FLAGS}")
994 set(old_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
995 set(CMAKE_REQUIRED_LIBRARIES "${FFT_LIBRARIES}")
997 check_function_exists(DftiCreateDescriptor TEST_MKL)
999 set(CMAKE_REQUIRED_FLAGS "${old_CMAKE_REQUIRED_FLAGS}")
1000 set(CMAKE_REQUIRED_LIBRARIES "${old_CMAKE_REQUIRED_LIBRARIES}")
1003 # Hack to help the user vary MKL settings until they work.
1004 # TODO Make this logic more useful.
1005 unset(TEST_MKL CACHE)
1006 message(FATAL_ERROR "Linking with MKL was requested, but was not successful. ${MKL_ERROR_MESSAGE}")
1009 # Set variables to signal that we have MKL available and should use it for FFTs.
1013 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
1014 MESSAGE(STATUS "Using external FFT library - Intel MKL")
1016 elseif(${GMX_FFT_LIBRARY} STREQUAL "FFTPACK")
1017 set(GMX_FFT_FFTPACK 1)
1018 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
1019 MESSAGE(STATUS "Using internal FFT library - fftpack")
1021 else(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1022 gmx_invalid_option_value(GMX_FFT_LIBRARY)
1023 endif(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1024 set(GMX_FFT_LIBRARY_PREVIOUS_VALUE ${GMX_FFT_LIBRARY} CACHE INTERNAL "Previous value for GMX_FFT_LIBRARY, so that we can detect when it changes.")
1026 # enable threaded fftw3 if we've found it
1027 if(FFTW3_THREADS OR FFTW3F_THREADS)
1028 add_definitions(-DFFT5D_FFTW_THREADS)
1031 include(gmxManageLinearAlgebraLibraries)
1033 # Whether GROMACS will really try to compile support for VMD plugins
1034 set(GMX_USE_PLUGINS OFF)
1036 if(GMX_LOAD_PLUGINS)
1037 if(CYGWIN OR NOT WIN32)
1038 # Native Windows does not have, nor need dlopen
1039 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
1040 include(gmxTestdlopen)
1041 gmx_test_dlopen(HAVE_DLOPEN)
1044 # so, should we use plug-ins?
1045 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
1048 "Found the ability to use plug-ins when building shared libaries, "
1049 "so will compile to use plug-ins (e.g. to read VMD-supported file "
1052 if(NOT GMX_VMD_PLUGIN_PATH)
1055 set(GMX_USE_PLUGINS ON)
1056 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
1057 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
1061 endif(GMX_LOAD_PLUGINS)
1062 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
1064 if(EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
1065 if(NOT CMAKE_CROSSCOMPILING)
1066 option(GMX_BUILD_MANPAGES "Build man pages" ON)
1068 message(STATUS "Building the man pages is not available when "
1069 "cross-compiling the developer version from git")
1072 #make sure source package contains all man pages
1073 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/man/man1/ngmx.1")
1074 message(FATAL_ERROR "Man pages are missing from source package.")
1077 mark_as_advanced(GMX_BUILD_MANPAGES)
1079 # Math and thread libraries must often come after all others when linking...
1081 list(APPEND GMX_EXTRA_LIBRARIES m)
1085 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
1086 "Path to swindirect.h")
1087 include_directories(${COREWRAP_INCLUDE_DIR})
1090 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
1091 # these are set after everything else
1092 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
1093 set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
1094 set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
1095 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
1096 set(CMAKE_SHARED_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
1098 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
1099 message("CMAKE_C_FLAGS: ${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
1100 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
1101 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
1102 message("CMAKE_CXX_FLAGS: ${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
1103 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
1104 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
1105 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
1106 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
1110 #Unset all OpenMP flags in case OpenMP was disabled either by the user
1111 #or because it was only partially detected (e.g. only for C but not C++ compiler)
1112 unset(OpenMP_C_FLAGS CACHE)
1113 unset(OpenMP_CXX_FLAGS CACHE)
1115 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
1116 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
1118 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
1120 ######################################
1121 # Output compiler and CFLAGS used
1122 ######################################
1123 get_compiler_info(C BUILD_C_COMPILER BUILD_CFLAGS)
1124 get_compiler_info(CXX BUILD_CXX_COMPILER BUILD_CXXFLAGS)
1126 get_cuda_compiler_info(CUDA_NVCC_COMPILER_INFO CUDA_NVCC_COMPILER_FLAGS)
1129 ########################################################################
1130 # Specify install locations
1131 ########################################################################
1132 if ( NOT DEFINED GMXLIB )
1135 set(LIB_INSTALL_DIR "${GMX_INSTALL_PREFIX}${GMXLIB}")
1136 set(BIN_INSTALL_DIR ${GMX_INSTALL_PREFIX}bin)
1137 set(DATA_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/gromacs)
1138 set(MAN_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/man)
1139 set(INCL_INSTALL_DIR ${GMX_INSTALL_PREFIX}include)
1141 set(GMXLIBDIR ${DATA_INSTALL_DIR}/top)
1143 ########################################################################
1144 # Set up binary and library suffixing
1145 ########################################################################
1148 "Use default suffixes for GROMACS binaries and libs (_d for double, _mpi for MPI; rerun cmake after changing to see relevant options)"
1150 gmx_dependent_cache_variable(
1152 "Suffix for GROMACS binaries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double)."
1154 "NOT GMX_DEFAULT_SUFFIX")
1155 gmx_dependent_cache_variable(
1157 "Suffix for GROMACS libraries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double)."
1159 "NOT GMX_DEFAULT_SUFFIX")
1160 if (GMX_DEFAULT_SUFFIX)
1161 set(GMX_BINARY_SUFFIX "")
1162 set(GMX_LIBS_SUFFIX "")
1164 set(GMX_BINARY_SUFFIX "_mpi")
1165 set(GMX_LIBS_SUFFIX "_mpi")
1168 set (GMX_BINARY_SUFFIX "${GMX_BINARY_SUFFIX}_d")
1169 set (GMX_LIBS_SUFFIX "${GMX_LIBS_SUFFIX}_d")
1171 if (NOT SUFFIX_QUIETLY)
1172 message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
1173 message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
1174 endif (NOT SUFFIX_QUIETLY)
1175 else(GMX_DEFAULT_SUFFIX)
1176 if (NOT SUFFIX_QUIETLY)
1177 message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
1178 message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
1179 endif (NOT SUFFIX_QUIETLY)
1180 endif(GMX_DEFAULT_SUFFIX)
1181 if (GMX_BUILD_MDRUN_ONLY)
1182 set(GMX_LIBS_SUFFIX "_mdrun${GMX_LIBS_SUFFIX}")
1184 set(SUFFIX_QUIETLY TRUE CACHE INTERNAL "")
1186 ##################################################################
1187 # Shared library settings
1188 ##################################################################
1189 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
1190 set(CMAKE_SKIP_BUILD_RPATH FALSE)
1191 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
1192 set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../${GMXLIB}")
1193 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
1195 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) #rpath supported for >10.4
1196 set(CMAKE_INSTALL_NAME_DIR "@rpath")
1197 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../lib")
1199 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
1203 #COPYING file: Only necessary for binary distributions.
1204 #Simpler to always install.
1205 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
1207 if(GMX_EXTERNAL_BOOST)
1208 include_directories(${Boost_INCLUDE_DIRS})
1210 include_directories(${CMAKE_SOURCE_DIR}/src/external/boost)
1211 # typeid not supported for minimal internal version
1212 # (would add significant amount of code)
1213 add_definitions(-DBOOST_NO_TYPEID)
1214 # TODO: Propagate the above settings to the installed CMakeFiles.txt template
1215 # (from share/template/)
1216 set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${INCL_INSTALL_DIR}/gromacs/external/boost")
1217 if (NOT GMX_BUILD_MDRUN_ONLY)
1218 install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
1219 DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
1220 COMPONENT development)
1224 if (GMX_BUILD_FOR_COVERAGE)
1225 # Code heavy with asserts makes conditional coverage close to useless metric,
1226 # as by design most of the false branches are impossible to trigger in
1227 # correctly functioning code. And the benefit of testing those that could
1228 # be triggered by using an API against its specification isn't usually
1230 add_definitions(-DNDEBUG -DBOOST_DISABLE_ASSERTS -DGMX_DISABLE_ASSERTS)
1233 if (NOT GMX_BUILD_MDRUN_ONLY)
1234 add_subdirectory(doxygen)
1235 add_subdirectory(share)
1236 add_subdirectory(scripts)
1238 add_subdirectory(src)
1240 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
1241 # Don't bother the user after the first configure pass.
1242 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
1243 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
1245 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
1247 #######################
1249 #######################
1251 "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
1252 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
1254 ###########################
1255 ADD_CUSTOM_TARGET(uninstall
1256 "${CMAKE_COMMAND}" -P
1257 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
1258 ###########################
1260 ########################################################################
1262 ########################################################################
1265 mark_as_advanced(BUILD_TESTING)
1268 #"check" target builds and runs all tests
1269 add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure)
1270 add_dependencies(check tests)
1271 # TODO: This would be better within tests/CMakeLists.txt
1272 if (NOT GMX_BUILD_MDRUN_ONLY)
1273 #gmxtests target builds all binaries required for running gmxtest
1274 add_custom_target(gmxtests DEPENDS gmx links)
1275 add_dependencies(check gmxtests)
1276 add_subdirectory(tests)
1278 #TODO: Add warning if NOT REGRESSIONTEST_PATH OR NOT GMX_XML that regression/unit tests are not run.